Characterizing the normal proteome of human ciliary body

Background

The ciliary body is the circumferential muscular tissue located just behind the iris in the anterior chamber of the eye. It plays a pivotal role in the production of aqueous humor, maintenance of the lens zonules and accommodation by changing the shape of the crystalline lens. The ciliary body is the major target of drugs against glaucoma as its inhibition leads to a drop in intraocular pressure. A molecular study of the ciliary body could provide a better understanding about the pathophysiological processes that occur in glaucoma. Thus far, no large-scale proteomic investigation has been reported for the human ciliary body.

Results

In this study, we have carried out an in-depth LC-MS/MS-based proteomic analysis of normal human ciliary body and have identified 2,815 proteins. We identified a number of proteins that were previously not described in the ciliary body including importin 5 (IPO5), atlastin-2 (ATL2), B-cell receptor associated protein 29 (BCAP29), basigin (BSG), calpain-1 (CAPN1), copine 6 (CPNE6), fibulin 1 (FBLN1) and galectin 1 (LGALS1). We compared the plasma proteome with the ciliary body proteome and found that the large majority of proteins in the ciliary body were also detectable in the plasma while 896 proteins were unique to the ciliary body. We also classified proteins using pathway enrichment analysis and found most of proteins associated with ubiquitin pathway, EIF2 signaling, glycolysis and gluconeogenesis.

Conclusions

More than 95% of the identified proteins have not been previously described in the ciliary body proteome. This is the largest catalogue of proteins reported thus far in the ciliary body that should provide new insights into our understanding of the factors involved in maintaining the secretion of aqueous humor. The identification of these proteins will aid in understanding various eye diseases of the anterior segment such as glaucoma and presbyopia.     

Characterization of dental pulp stem/stromal cells of Huntington monkey tooth germs

Background

Activation by extracellular ligands of G protein-coupled (GPCRs) and tyrosine kinase receptors (RTKs), results in the generation of second messengers that in turn control specific cell functions. Further, modulation/amplification or inhibition of the initial signalling events, depend on the recruitment onto the plasma membrane of soluble protein effectors. High throughput methodologies to monitor quantitatively second messenger production, have been developed over the last years and are largely used to screen chemical libraries for drug development. On the contrary, no such high throughput methods are yet available for the other aspect of GPCRs regulation, i.e. protein translocation to the plasma membrane, despite the enormous interest of this phenomenon for the modulation of receptor downstream functions. Indeed, to date, the experimental procedures available are either inadequate or complex and expensive.

Results

Here we describe the development of a novel conceptual approach to the study of cytosolic proteins translocation to the inner surface of the plasma membrane. The basis of the technique consists in: i) generating chimeras between the protein of interests and the calcium (Ca²⁺)-sensitive, luminescent photo-protein, aequorin and ii) taking advantage of the large Ca²⁺ concentration [Ca²⁺] difference between bulk cytosolic and the sub-plasma membrane rim.

Conclusion

This approach, that keeps unaffected the translocation properties of the signalling protein, can in principle be applied to any protein that, upon activation, moves from the cytosol to the plasma membrane. Thus, not only the modulation of GPCRs and RTKs can be investigated in this way, but that of all other proteins that can be recruited to the plasma membrane also independently of receptor activation. Moreover, its automated version, which can provide information about the kinetics and concentration-dependence of the process, is also applicable to high throughput screening of drugs affecting the translocation process.     

Effect of different temperature on starch synthase activity in excised grains of wheat cultivars

Excised grains of wheat (Triticum aestivum) varieties HD 2285 (relatively tolerant) and HD 2329 (susceptible type) were incubated for 1 hr at 15 degrees, 25 degrees, 35 degrees and 45 degrees C. In an another treatment, excised grains were incubated for 1 hr at increasing temperature (15 degrees, 25 degrees, 35 degrees and 45 degrees C) continuously, thus exposing the grains to gradual rise in temperature. The above treated grains were then analysed for the activity of soluble starch synthase (SSS) and granule bound starch synthase (GBSS) assayed at 20 degrees C. SSS activity decreased as the pre-exposure temperature was higher, though the tolerant variety showed lesser decrease. Decrease in SSS activity was lesser when excised grains were exposed to gradual rise in temperature from 15 degrees to 45 degrees C as compared to direct exposure to 45 degrees C. Pre-exposure of excised grains to different temperatures however, had no significant effect on GBSS activity.     

Photosynthetic response of wheat and sunflower cultivars to long-term exposure of elevated carbon dioxide concentration

Wheat (Triticum aestivum L. cv. HD 2329 and DL 1266-5) and sunflower (Helianthus annuus L. cv. MSFH 17 and MRSF 1754) plants were grown in field under atmospheric (360±10 cm³ m⁻³, AC) and elevated (650±50 cm³ m⁻³, EC) CO₂ concentrations in open top chambers for entire period of growth and development till maturity. Net photosynthetic rate (P _N) of wheat cvs. when compared at the same internal CO₂ concentration (C _i), by generating P _N/C _i curves, showed lower P _N in EC plants than in AC ones. EC-grown wheat cultivars also showed a lesser response to irradiance than AC plants. In sunflower cultivars, P _N/C _i curves and irradiance response curves were not significantly different in AC and EC plants. CO₂ and irradiance responses of photosynthesis, therefore, further revealed a down-regulation of _{P N} in wheat but not so in sunflower under long-term CO₂ enrichment. Wheat cvs. accumulated in leaves mostly sugars, whereas sunflower accumulated mainly starch. This further strengthened the view that accumulation of excess assimilates in the leaves under EC as starch is not inhibitory to _{P N}.     

Deep sequencing reveals clonal evolution patterns and mutation events associated with relapse in B-cell lymphomas

Background

Molecular mechanisms associated with frequent relapse of diffuse large B-cell lymphoma (DLBCL) are poorly defined. It is especially unclear how primary tumor clonal heterogeneity contributes to relapse. Here, we explore unique features of B-cell lymphomas - VDJ recombination and somatic hypermutation - to address this question.

Results

We performed high-throughput sequencing of rearranged VDJ junctions in 14 pairs of matched diagnosis-relapse tumors, among which 7 pairs were further characterized by exome sequencing. We identify two distinctive modes of clonal evolution of DLBCL relapse: an early-divergent mode in which clonally related diagnosis and relapse tumors diverged early and developed in parallel; and a late-divergent mode in which relapse tumors developed directly from diagnosis tumors with minor divergence. By examining mutation patterns in the context of phylogenetic information provided by VDJ junctions, we identified mutations in epigenetic modifiers such as KMT2D as potential early driving events in lymphomagenesis and immune escape alterations as relapse-associated events.

Conclusions

Altogether, our study for the first time provides important evidence that DLBCL relapse may result from multiple, distinct tumor evolutionary mechanisms, providing rationale for therapies for each mechanism. Moreover, this study highlights the urgent need to understand the driving roles of epigenetic modifier mutations in lymphomagenesis, and immune surveillance factor genetic lesions in relapse.

Electronic supplementary material

The online version of this article (doi:10.1186/s13059-014-0432-0) contains supplementary material, which is available to authorized users.     

Photosynthetic acclimation to elevated CO2 in wheat cultivars

Wheat (T. aestivum) cvs. Kalyansona and Kundan grown under atmospheric (CA) and elevated CO₂ concentrations (650±50 cm³ m^-3 - CE) in open top chambers were examined for net photosynthetic rate (PN), stomatal limitation (l _s) of P _N, ribulose-1,5-bisphosphate carboxylase (RuBPC) activity, and saccharide content of the leaves. The P _N values of both CA- and CE-grown plants compared at the same CO₂ concentration showed a down regulation under CE at the post-anthesis stage. The negative acclimation of P _N appeared to be due to both stomatal and mesophyll components, and the RuBPC activity got also adjusted. There was a decrease in activation state of RuBPC under CE. In connection with this, an increased accumulation of saccharides in wheat leaf under CE was observed. Kalyansona, owing to its larger sink potential in terms of the number of grains, showed a greater enhancement under CE in both post-ear emergence dry matter production and grain yield. Under CE, this cultivar also showed a lower down regulation of P _N than Kundan. This revised version was published online in June 2006 with corrections to the Cover Date.